Schwarz-Finsterle J, Stein S, Grossmann C, Schmitt E, Trakhtenbrot L, Rechavi G, Amariglio N, Cremer C, Hausmann M.
Comparison of triple helical COMBO-FISH and standard FISH by means of quantitative microscopic image analysis of abl/bcr positions in cell nuclei.
J Biochem Biophys Methods. 2007;70:397-406.  (PubMed)

Gutermann A, Mayer E, von Dehn-Rothfelser K, Breidenstein C, Weber M, Muench M, Gungor D, Suehnel J, Moebius U, Lechmann M.
Efficacy of oncolytic herpesvirus NV1020 can be enhanced by combination with chemotherapeutics in colon carcinoma cells.
Hum Gene Ther. 2006;17:1241-53. (PubMed)

Nolte O, Müller M, Häfner B, Knemeyer JP, Stöhr K, Wolfrum J, Hakenbeck R, Denapaite D, Schwarz-Finsterle J, Stein S, Schmitt E, Cremer C, Herten DP, Hausmann M, Sauer M.
Novel singly labelled probes for life science applications (SMART PROBES).
In: Biophotonics: Visions for Better Health Care(J. Popp, M. Strehle, Eds.), Wiley-VCH, 2006, 167-230.

Glockner G, Schulte-Spechtel U, Schilhabel M, Felder M, Suhnel J, Wilske B, Platzer M.
Comparative genome analysis: selection pressure on the Borrelia vls cassettes is essential for infectivity.
BMC Genomics. 2006;7:211. (PubMed)

Hausmann M, Hildenbrand G, Schwarz-Finsterle J, Spöri U, Schneider H, Schmitt E, Cremer C.
New technologies measure genome domains - High resolution microscopy and novel labeling procedures enable 3-D studies of the functional architecture of gene domains in cell nuclei.
Biophotonics Int. 2005;12,34-37.

Riemann RN, Zacharias M.
Refinement of protein cores and protein-peptide interfaces using a potential scaling approach.
Protein Eng Des Sel. 2005;18,465-476.  (PubMed)

Schwarz-Finsterle J, Stein S, Grossmann C, Schmitt E, Schneider H, Trakhtenbrot L, Rechavi G, Amariglio N, Cremer C, Hausmann M.
COMBO-FISH for focussed fluorescence labelling of gene domains: 3D-analysis of the genome architecture of abl and bcr in human blood cells.
Cell Biol Int. 2005;29,1038-1046. (PubMed)

Imhof D, Wieligmann K, Hampel K, Nothmann D, Zoda MS, Schmidt-Arras D, Zacharias M, Böhmer FD, Reissmann S.
Design and biological evaluation of linear and cyclic phosphopeptide ligands of the N-terminal SH2 domain of protein tyrosine phosphatase SHP-1.
J. Med. Chem. 2005;48,1528-1539. (PubMed)

Romualdi A, Siddiqui R, Glöckner G, Lehmann R, Sühnel J.
GenColors: accelerated comparative analysis and annotation of prokaryotic genomes at various stages of completeness.
Bioinformatics. 2005;21,3669-3672.  (PubMed)

Wieland GD, Nehmann N, Müller D, Eibel H, Siebenlist U, Sühnel J, Zipfel PF, Skerka C.
Early growth response proteins EGR-4 and EGR-3 interact with immune inflammatory mediators NF-kappaB p50 and p65.
J. Cell Science. 2005;118,3203-3212. (PubMed)

Meyer M, Hocquet A, Sühnel J.
Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads.
J. Comp. Chem. 2005;26,352-364. (PubMed)

Monajembashi S, Rapp A, Schmitt E, Dittmar H, Greulich KO, Hausmann M.
Spatial association of homologous pericentric regions in human lymphocyte nuclei during repair.
Biophys. J. 2005;88,2309-2322. (PubMed)

Szymoszek A, Zacharias M.
Reduced protein model as a tool in the homology modeling.
Internet. Electron. J. Mol. Des., 2004, November 29 - December 12 (Journal Link)

Villescas-Diaz G, Zacharias M.
Efficient search on energy minima for structure prediction of nucleic acid motifs.
J. Biomol. Struct. Dyn. 2004;22,355-364. (PubMed)

Schönecker B, Zheldakova T, Lange C, Günther W, Görls H, Bohl M.
Intramolecular gamma-hydroxylations of nonactivated C-H bonds with copper complexes and molecular oxygen.
Chemistry. 2004;10,6029-6042.  (PubMed)

Glöckner G, Lehmann R, Romualdi A, Pradella S, Schulte-Spechtel U, Schilhabel M, Wilske B, Sühnel J, Platzer M.
Comparative analysis of the Borrelia garinii genome.
Nucleic Acids Res. 2004;32,6038-6046. (PubMed)

Riemann NM, Zacharias M.
Reversible scaling of dihedral angle barriers during molecular dynamics to improve structure prediction of cyclic peptides.
J. Pept. Res. 2004;63,354-364. (PubMed)

Frank C, Burkhardt C, Imhof D, Ringel J, Zschörnig O, Wieligmann K, Zacharias M, Böhmer FD.
Effective dephosphorylation of Src substrates by SHP-1.
J. Biol. Chem. 2004:279,11375-11383. (PubMed)

Groten JP, Cassee FR, van Bladeren PJ, de Rosa C, Feron VJ, Sühnel J.
Mischungen chemischer Stoffe.
In: Lehrbuch der Toxikologie, (Hrsg. H. Marquardt, S. G. Schäfer),ISBN: 3804717772,
Wissenschaftliche Verlagsgesellschaft, Stuttgart, 2004, Kap. 13, pp. 287-302 [Amazon]

Meyer M, Sühnel J.
Base polyad motifs in nucleic acids - Biological significance, occurrence in three-dimensional experimental structures and computational studies. 
In: Computational Chemistry: Reviews of Current Trends, Vol. 8, (Ed. J. Leszczynski), ISBN: 981-238-702-1,
World Scientific Publishing Company, 2003, Chapter 4, pp. 161-208.

Kronen M, Görls H, Nguyen HH, Reissmann S, Bohl M, Sühnel J, Gräfe U.
Crystal structure and conformational analysis of ampullosporin A.
J. Peptide Sci. 2003;9,729-744. (PubMed)

Villescas-Diaz G, Zacharias M.
Sequence context dependence of tandem guanine:adenine mismatch conformations in RNA: a continuum solvent analysis.
Biophys J. 2003;85,416-425. (PubMed)

Hausmann M, Winkler R, Hildenbrand G, Finsterle J, Weisel A, Rapp A, Schmitt E, Janz S, Cremer C.
COMBO-FISH: specific labeling of nondenatured chromatin targets by computer-selected DNA oligonucleotide probe combinations.
BioTechniques 2003, 35, 564-577. (PubMed)

Meyer M, Sühnel J. [not peer-reviewed]
Computational studies on base tetrad motifs in nucleic acid structures - Quantum chemistry helps to understand biology.
Berichte des IZWR (Friedrich-Schiller-Universität Jena), Band, 2003, 43-60. [PDF]

Meyer M, Sühnel J.
Self-association of isoguanine nucleobases and molecular recognition of alkaline ions: Tetrad versus pentad structures
J. Phys. Chem. A. 2003;107,1025-1031

Meyer M, Sühnel J.
Interaction of cyclic cytosine-, guanine-, thymine-, uracil- and mixed guanine-cytosine base tetrads with K+, Na+ and Li+ ions -- a density functional study.
J. Biomol. Struct. Dyn. 2003;20,507-518. (PubMed)

Louit G, Hoquet A, Ghomi M, Meyer M, Sühnel J.
Guanine tetrads interacting with metal ions. An AIM topological analysis of the electron density.
PhysChemComm. 2003;6,1-5.

Pal D, Sühnel J, Weiss MS.
New principles of protein structure: Nests, eggs and what next? 
Angewandte Chem. Int. Ed. 2002;41,4663-4665. (PubMed)

Louit G, Hoquet A, Ghomi M, Meyer M, Sühnel J.
Are guanine tetrads stabilised by bifurcated hydrogen bonds: An AIM topological analysis of electron density.
PhysChemComm. 2002;5,94-98

Rahn K, Sühnel J. [not peer-reviewed]
Das Jenaer Centrum für Bioinformatik.
BIOforum. 2002;7-8,454-455.  [PDF]

Sühnel J.
Beyond nucleic acid base pairs: From triads to heptads.
Biopolymers (Nucleic Acid Sciences). 2002;61,32-51. (Pubmed)

Reichert J, Sühnel J.
The IMB Jena Image Library of Biological Macromolecules - 2002 update.
Nucleic Acids Research. 2002;30,253-254.  (Pubmed)

Meyer M, Schneider C, Brandl M, Sühnel  J.
Cyclic adenine-, cytosine-, thymine- and mixed guanine-cytosine- base tetrads in nucleic acids viewed from a quantum-chemical and force field perspective.
J. Phys. Chem. A. 2001;105,11560-11573

Meyer M, Brandl M, Sühnel J. 
Are guanine tetrads stabilized by bifurcated hydrogen bonds?
J. Phys. Chem. A. 2001;105,8223-8225.

Weiss MS, Brandl M, Sühnel J, Pal D, Hilgenfeld R.
More hydrogen bonds for the (structural) biologist.
Trends Biochem. Sci. 2001;26,521-523.(Pubmed)

Groten JP, Feron VJ, Sühnel J.
Toxicology of simple and complex mixtures.
Trends Pharmacol. Sci. 2001;22,316-322. (PubMed)

Brandl M, Weiss MS, Jabs A, Sühnel J, Hilgenfeld R.
C-H...pi-interactions in proteins.
J. Mol. Biol. 2001;307,357-377. (PubMed)

Schneider C, Brandl M, Sühnel J.
Molecular dynamics simulation reveals conformational switching of water-mediated uracil-cytosine base-pairs in an RNA duplex.
J. Mol. Biol. 2001;305,659-667. (PubMed)

Brandl M, Meyer M, Sühnel J.
Quantum-chemical analysis of C-H...O and C-H...N interactions in RNA base pairs--H-bond versus anti-H-bond pattern.
J. Biomol. Struct. Dyn. 2001;18,545-555. (PubMed)

Meyer M, Steinke T, Brandl M, Sühnel J.
Density functional study of guanine and uracil quartets and of guanine/metal ion complexes.
J. Comp. Chem. 2001;22,109-124.

Brandl M, Meyer M, Sühnel J. 
Water-mediated base pairs in RNA - A quantum-chemical study. 
J. Phys. Chem. A, 2000, 104, 11177-11187

Reichert J, Jabs A, Slickers P, Sühnel J.
The IMB Jena Image Library of biological macromolecules. 
Nucleic Acids Res. 2000:28,246-249. (PubMed)) | Supplementary Material

Cassee FR, Sühnel J, Groten JP, Feron V. 
Toxicology of chemical mixtures. 
In: General and Applied Toxicology, 2nd edition, B. Ballantyne, T. C. Marrs, T. Syverson (Eds.), MacMillan Reference Ltd., Oxford, 1999, 2nd Ed., Vol. 1, ch. 14, pp. 303-319 .

Schneider C, Sühnel J.
A molecular dynamics simulation of the flavin mononucleotide-RNA aptamer complex. 
Biopolymers, 1999;50,287-302.  (PubMed)

Sühnel J.
Computer modeling of protein, nucleic acid, and drug structures.
In: Microsystem Technology: A Powerful Tool for Biomolecular Studies, H.-P. Saluz, M. Köhler (Eds.), Birkhäuser Verlag, Basel, 1999, 475-505.

Dressler V, Müller G, Sühnel J.
CombiTool--a new computer program for analyzing combination experiments with biologically active agents.
Comput Biomed Res. 1999;32,145-160.  (PubMed)

Brandl M, Meyer M, Sühnel J. 
Quantum-chemical study of a water-mediated uracil-cytosine base pair.
J. Amer. Chem. Soc. 1999;121,2605-2606.

Brandl M, Lindauer K, Meyer M, Sühnel J. 
C-H...O and C-H...N interactions in RNA structures.
Theor. Chem. Acc. 1999;101,103-113.
(Special Issue of the European Conference 'Computational Chemistry and the Living World: From Sequence to Function', Chambery / France, April 20-24, 1998)

Meyer M, Wohlfahrt G, Knäblein J, Schomburg D.
Aspects of the mechanism of catalysis of glucose oxidase: a docking, molecular mechanics and quantum chemical study.
J Comput Aided Mol Des. 1998;12, 425-440. (PubMed)

Meyer M, Schomburg  D.
Protein interactions.
In: Biotechnology (Eds. H. J. Rehm, G. Reed), Vol. 5, Recombinant Proteins, Monoclonal Antibodies and Therapeutic Genes, VCH, Weinheim, 1998, 48-68.

Slickers P, Hillebrand M, Kittler L, Löber G, Sühnel J.
Molecular modelling and footprinting studies of DNA minor groove binders: bisquaternary ammonium heterocyclic compounds. 
Anti-Cancer Drug Des.1998;13,463-488. (PubMed)

J. Reichert, A. Jabs, J. Sühnel .
Virtual Reality Modeling. 
Nachrichten aus Chemie, Technik und Laboratorium. 1998;46,A64-A68. (preprint version in PDF format)

Sühnel  J.
Parallel dose-response curves in combination experiments.
Bull. Math. Biol. 199860,197-213. (PubMed)

S. A. Cassidy, P. Slickers, J. O. Trent, D. C. Capaldi, P. D. Roselt, C. B. Reese, S. Neidle, K. R. Fox 
Recognition of GC base pairs by triplex forming oligonucleotides containing nucleosides derived from 2-aminopyridine.
Nucleic Acids Res. 199715,4891-4898. (PubMed)

Meyer M, Sühnel  J.
Quantum-chemical ab initio study on the adenine-difluorotoluene complex--a mimic for the adenine-thymine base pair.
J. Biomol. Struct. Dyn. 1997;15,619-624. (PubMed)

Vogt T, Zimmermann E, Grimm R, Meyer M, Strack  D.
Are the characteristics of betanidin glucosyltransferases from cell-suspension cultures of Dorotheanthus bellidiformis indicative of their phylogenetic relationship with flavonoid glucosyltransferases? 
Planta. 1997;203,349-361.  (PubMed)

Sühnel J, Hermann G, Dornberger U, Fritzsche H.
Computer analysis of phytochrome sequences and reevaluation of the phytochrome secondary structure by Fourier transform infrared spectroscopy. Biochim. Biophys. Acta. 1997;1340,253-267. (PubMed)

Sühnel  J.
Views of RNA on the World Wide Web.
Trends Genet. 1997;13,206-207.  PubMed

Sühnel J.
Virtual reality modeling for structural biology.
In: Proceedings of the German Conference on Bioinformatics, GCB '96. Lecture notes in computer science Vol. 1278, (R. Hofestädt, T. Lengauer, M. Löffler, D. Schomburg, eds.) Springer-Verlag Berlin, 1997, 189-198. (Book Link)

Lindauer K, Bendic C, Sühnel  J.
HBexplore--a new tool for identifying and analysing hydrogen bonding patterns in biological macromolecules.
Comput. Appl. Biosci. 1996, 12, 281-289. (PubMed)

Sühnel  J.
Zero interaction response surfaces for combined-action assessment. 
Food Chem. Toxicol. 1996;34,1151-1153. (PubMed)

Sühnel  J.
Image library of biological macromolecules. 
Comput. Appl. Biosci. 1996;12, 227-229.  (PubMed)

Recknagel R-D, Weller K, Köhler  J-M.
A simple method to forecast good promoters of Escherichia coli by means of doublet frequencies.
J. Theor. Biol. 1993, 162, 75-80. (PubMed)

Sühnel, J.
The Marcus cross relation for hydrogen transfer reactions.
J. Phys. Org. Chem. 1993, 6, 281-286

Sühnel  J.
Evaluation of interaction in olfactory and taste mixtures.
Chemical Senses. 1993;18,131-149.

Greco WR, Unkelbach H-D, Pöch G, Sühnel J, Kundi M, Bödeker  W.
Consensus on concepts and terminology for combined-action assessment: The Saariselkä agreement
Archives of Complex Environmental Studies. 1992;4,65-69 .

Sühnel  J.
Assessment of the interaction of biologically active agents by means of the isobole approach: Fundamental assumptions and recent developments.
Archives of Complex Environmental Studies. 1992;4,35-44 .

Sühnel  J.
Re: W. R. Greco et al., Application of a new approach for the quantitation of drug synergism to the combination of cis-diamminedichloroplatinum and 1-beta-D-arabinofuranosylcytosine.
Cancer Res. 1992;52,4560-4561. (PubMed)

Sühnel  J.
Comment on the paper: A three-dimensional model to analyze drug-drug interactions. Prichard, M.N. and Shipman, C., Jr. (1990) Antiviral Res. 14, 181-206.
Antiviral Res. 1992;17,91-93. (PubMed)

Sühnel  J.
Zero interaction response surfaces, interaction functions and difference response surfaces for combinations of biologically active agents.
Arzneimittelforschung. 1992;42,1251-1258. (PubMed)

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